The British government said yesterday that Tehran could still be developing a nuclear weapon, and called into question a key American intelligence finding that work on building an Iranian bomb had stopped in 2003.

For the first time, a senior British diplomat cast doubt on the US National Intelligence Estimate published last November which reported "with high confidence" that Tehran's nuclear weapons programme had been halted in autumn 2003. The NIE also judged "with moderate confidence" that the programme had not been restarted.

The intelligence report blocked momentum towards US military action and delayed the passing of a third sanctions resolution against Tehran - a mild version of which was approved this week in an effort to persuade Iran to suspend enrichment of uranium. But the senior British diplomat claimed there was no serious evidence that Iran's efforts to build a nuclear weapon had halted.

"When the NIE came out many of us were surprised at how emphatic the writers of it were - that all the activity stopped in 2003 and the medium confidence that it had not been resumed," the diplomat said on condition of anonymity. "I haven't seen any intelligence that gives me even medium confidence that these programmes haven't resumed. It's an uncertain picture."

The comments appeared to reflect the findings of an independent British assessment of intelligence on Iran's nuclear programme, completed after the American assessment was published.

The diplomat pointed to evidence against Iran presented in Vienna last week by Olli Heinonen, the chief investigator at the International Atomic Energy Agency.

According to a summary of the Heinonen meeting obtained by the Guardian, the Finnish investigator presented an organisational chart linking a variety of nuclear weapons projects. A document on the organisation "includes 10 to 15 pages of instructions on how to communicate, setting out in particular rules for correspondence excluding the use of people's names". Another document was a report on a weapons project for a period up to January 14 2004, months after the end date suggested in the NIE.

Heinonen stressed that the IAEA was unable to verify the authenticity of the documents.

The evidence has been met with scepticism by several members of the IAEA, who point to the debacle over WMD intelligence on Iraq.

The senior British diplomat said, however: "Just because we got it wrong on Iraq doesn't mean we're getting it wrong on Iran."

Heinonen also said IAEA inspectors had not been allowed to question an Iranian defence ministry official, Mohsen Fakrizadeh, who allegedly led the weaponisation effort. Simon Smith, Britain's representative on the IAEA board, said Heinonen's evidence was neither new, nor substantiated. But Smith told the Guardian: "The [IAEA investigators] wanted to drive home to the board that this was not a few scraps of paper or overheard conversations. It was a substantial package of evidence."

That package was dismissed by Iran as either fabricated or irrelevant. Tehran insists it has not attempted to make weapons and is only enriching uranium to generate energy for peaceful purposes. President Mahmoud Ahmadinejad yesterday rejected calls for further negotiations with the EU's foreign policy chief, Javier Solana, saying his officials would henceforth only talk to IAEA representatives.

The forcefulness of Heinonen's presentation caused rifts within the IAEA, irritating the agency's director general, Mohamed ElBaradei, who has sought to defuse international tensions over Iran's nuclear programme.

Addressing the IAEA board on Monday, ElBaradei said his inspectors had resolved all but one of the unanswered questions over Iran's nuclear programme, the exception being the weaponisation studies.

However, Smith, speaking on behalf of Britain, Germany and France at the IAEA board yesterday, said Iran's cooperation had been "abysmal". "Over a wide range of issues on which the agency asked for clarification the answers are less than satisfactory," he said.

A sanctions resolution passed by the UN security council on Monday tightened existing measures against Iran, extending a travel ban and assets freeze on individuals and firms linked to the nuclear programme, and added two Iranian banks to an international watch list for involvement in proliferation.

EU officials are due to meet this month to decide whether to go further than the UN resolution in applying punitive measures against Iran.